My personal theory is that Arnold's "maze" is all about transferring the human consciousness into a host. I think Arnold's obsession with this came from that it may have been his son that died, as Ford said his life was marked by personal tragedy. Bernard may have been his attempt at transferring the human consciousness into a host and/or interference by Ford. It would make sense that if it was Arnold's son that died that he would be obsessed at bringing him back to life. The reason I think this may be feasible, there's a line that Ford says to Tommy before uploading the Wyatt backstory, that "like all great stories, one that is rooted in truth". Perhaps Ford uploaded Arnold's backstory to Bernard as a means of control. However there's a line where Ford talks about the medical technology can save anyone, the only question is that statement which seems to have been given in the most recent timeline, would it be true 35 years ago when the incident occurred regarding Arnold.
I'm torn on if the MIB is William or Logan. I've heard good theories on both, that Logan could be MIB and Tommy is William with a failed attempt at transferring his consciousness. There's several thematic events to suggest that William may be tommy, such as they both enter the park asleep on a train. They bump into the same person on the street. They both pick up the dropped can from Dolores on the street. It could be that Tommy's loop is actually a continuation of William's unfinished tale.
On the other hand there's a line that Logan says to William that "this place seduces everyone eventually, it will get to you too, and I can't ******* wait to meet that guy." this would suggest that William could become the person he despises the most....Logan.
The show throws you on so many loops that I can see it going in any number of directions.